Variable Loop In Trna Role

plays an important role in the process ofcedon recognition by certain tRNAs.

tRNAs Share a Common Secondary Structure that Resembles a Clover leaf

As we saw in Chapter 6, RNA molecules typically contain regions of self-complementarity that enable them to form limited stretches of double helix that are held together by base pairing. Other regions of RNA molecules have no complement and hence, are single-stranded. tRNA molecules exhibit a characteristic pattern of single-stranded and double-stranded regions (secondary structure) that can he illustrated as a cioverieaf [Figure 14-4), The principal features of the tRNA rloveiieaf are an acceptor stem; three stem-loops, which are referred to as the ^FLJ loop, the D loop, and the auticodon loop; and a fourth variable loop. Descriptions of each of these features follows:

• The acceptor stem, so-named because it is the site of attachment of the amino arid, is formed by pairing between the 5' and 3' ends of the tRNA molecule. The 5'-CCA-3' sequence at the extreme end of the molecule protrudes from this double-stranded stem.

• The loop is so-named because of the characteristic presence of the unusual base in the loop, The modified base is often found within the sequence 5'-TWCG-3'.

• The D loop takes its name from the characteristic presence of dihydrouridines in the loop.

• The auticodon loop, as its name implies, contains the anticodon, a tbree-nucleotide-long decoding element that is responsible tor recognizing the codon by base-pairing with the mRNA, The anticodon is bracketed on the 3' end by a purine and on its 5' end by uracil.

• The variable loop sits between the anticodon loop and the "tyU loop, and, as its name implies, varies in size from 3 to 21 bases.

FIGURE 14-4 Cioverieaf representation of the secondary structure of tRNA. tn this representation of a tRNA: the base-paiimg between different parti of the tRNA are indicated by the dotted red tines.

acceptor arm

D loop

D loop

anticodon loop variable loop anticodon anticodon loop variable loop

VU roop anticodon

Attachment of Amino Acids to tHNA 417

Attachment of Amino Acids to tHNA 417

FIGURE 14-5 Conversion between the cloverleaf and the actual three-dimensional structure of a tRNA. (a) Cloverleaf representation. <b) L-shaped representation showing the tocation ot the base-paired regions of the final folded tRNA. (c) Ribbon representation ot the actual folded structure of a tRNA. Note that although this diagram illustrates how the actual tRNA structure is related to the doverleaf representation, a tRNA does not attain its final structure by first base-painng and then folding into an L-shape.

FIGURE 14-5 Conversion between the cloverleaf and the actual three-dimensional structure of a tRNA. (a) Cloverleaf representation. <b) L-shaped representation showing the tocation ot the base-paired regions of the final folded tRNA. (c) Ribbon representation ot the actual folded structure of a tRNA. Note that although this diagram illustrates how the actual tRNA structure is related to the doverleaf representation, a tRNA does not attain its final structure by first base-painng and then folding into an L-shape.

tRNAs Have an L-Shaped Three-Dimensional Structure

The cloverleaf reveals regions of self-complementarity within tRNAs. What is the actual three-dimensional configuration of this adaptor molecule? X-ray crystallography reveals on L-shaped tertiary structure in which the terminus of the acceptor stem is at one end of the molecule and the anticodon loop is about 70 A away at the other end. To understand the relationship of this L-shaped structure (depicted as an upside-down L in Figure 14-5) to the cloverleaf, consider the following: the acceptor stem and the stem of the "^U loop form an extended helix in the final tRNA structure. Similarly, the anticodon stem and the stem of the D loop form a second extended helix. These two extended helices align at a right angle to each other, with the D loop and the ^'U loop coming together. In the final image, the two extended helices adopt their proper helical configuration.

Three kinds of interactions stabilize this L-shaped structure. The first is hydrogen bonds between bases in different helical regions that are hrought near each other in three-dimensional space by the tertiary structure. These are generally unconventional (non-Watson-Crick) bonding. The second are interactions between the bases and the sugar-phosphate backbone. The third kind of stabilizing interaction is the additional base stacking gained from formation of the two extended regions of base pairing.

ATTACHMENT OF AMINO ACIDS TO tRNA

tRNAs Are Charged by the Attachment of an Amino Acid to the 3' Terminal Adenosine Nucleotide via a High-Energy Acyl Linkage tRNA molecules to which an amino acid is attached are said to be charged, and tRNAs that lack an amino acid are said to be uncharged. Charging requires an acyl linkage between the carboxyl group of the amino acid and the 2'- or 3'-hydroxyl group (see below) of the adenosine nucleotide that protrudes from the acceptor stern. This acyl linkage is considered to he a high-energy bond in that its hydrolysis results in b large change in free energy. This is significant for protein synthesis; the energy released when the bond is broken helps drive the formation of the peptide honds that link amino acids to each other in polypeptide chains, as ive will see below.

Aminoacyl tRNA Synthetases Charge tRNAs in Two Steps

All aminoacyl tRNA synthetases attach an amino acid to a tRNA in two enzymatic steps (Figure 14-6). Step one is adenylylation in which the amino acid reacts with ATP to become adenylylated with the con-

figure 14-6 The two steps of aminoacyl-tRNA charging, (a) Adenyfyiarton of amino aad. (fc>) Transfer of the adenylylated amino add to tRNA. "the process shown ts for a dass II (RNA synthase.

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